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[Preprint]. 2023 Jan 22:2023.01.21.525036. [Version 1] doi: 10.1101/2023.01.21.525036

Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis

Elvira Mennillo, Yang Joon Kim, Iulia Rusu, Gyehyun Lee, Leah C Dorman, Faviola Bernard-Vazquez, Jared L Bain, Ravi Patel, Christopher Andersen, Arjun Rao, Stanley Tamaki, Jessica Tsui, Alan Shen, Mohammad Naser, Walter Eckalbar, Soo-jin Cho, Kendall Beck, Najwa El-Nachef, Sara Lewin, Daniel R Selvig, Jonathan P Terdiman, Uma Mahadevan, David Y Oh, Gabriela K Fragiadakis, Angela Pisco, Alexis J Combes, Michael G Kattah
PMCID: PMC9882264  PMID: 36711576

ABSTRACT

Ulcerative colitis (UC) is an inflammatory intestinal disorder driven by mucosal immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin monoclonal antibody that is effective for treating UC. VDZ is thought to primarily inhibit lymphocyte trafficking to the intestine, but its effect on other cell subsets is less well characterized. To identify the inflammatory cells that contribute to colitis and respond to VDZ, we performed a single-cell transcriptomic and proteomic analysis of peripheral blood and colonic biopsies in healthy controls (HC) and patients with UC on either aminosalicylates or VDZ. We identified mononuclear phagocytes (MNPs) as a primary target of VDZ, with comparatively modest effects on lymphocytes. Spatial proteomics and transcriptomics demonstrated increased density and proximity of MNP and fibroblast subsets in UC biopsies when compared to HC, with inhibition by VDZ. VDZ non-responders were enriched for activated fibroblast and MNP signatures in a validation cohort.

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